Evolution, transitions, and volvocine algae

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I am a biologist who studies the evolution of biological complexity using Volvox and related algae as a study system. I blog about evolutionary biology, astrobiology, philosophy of biology, skepticism, academia and academic publishing, intelligent design and other forms of creationism, and whatever else happens to be on my mind.Read More…

EVENTS

It’s not evolution, just adaptation

…”evolve” is not the correct term. The microbes adapted. – Cornelius Hunter

We heard several accusations during the recent Presidential campaign that one or the other candidate, or an interviewer, had taken a quote out of context. Of course, every quote is taken out of context. That’s what a quote is; otherwise it’s just the whole speech, or interview, or whatever. The important question is whether or not it’s taken out of context in a way that changes its meaning.

One thing I don’t do, and never have done, on this blog is intentionally misrepresent other people’s positions. The quote above, from a recent post by Cornelius Hunter on Evolution News and Views, means just what it says. He really is arguing that microbial adaptation observed in Lenski-style experiments is not evolution.

In some sense, the confusion is understandable. “Adapt,” like “theory” and “random,” means something different in biology from its everyday use: I’m waiting for a flight to Colorado, where I plan (among other things) to run in a turkey trot. My performance will probably suffer because I’ve adapted to living near sea level. [update: it did suffer]

Every evolutionary biologist reading this just cringed a little.

Why? Because in biology, adapt means something like ‘evolve due to selection.’ Adaptation is evolutionary change, which occurs in populations over generations, not within individuals within generations.

My expertise is specifically in evolution — its history, philosophy, theology, and of course the underlying science. Too often evolution courses lack these four components, but they are crucial to genuine understanding.

I saw Dr. Baym present this work at the recent ASM Conference on Experimental Microbial Evolution. What they did, in a nutshell, is set up very large (120 x 60 cm), rectangular petri dishes with increasing levels of antibiotic from the ends to the center:

Figure 1A from Baym et al. 2016. Setup of the four-step gradient of trimethoprim. Antibiotic is added in sections to make an exponential gradient rising inward. Successive regions of black-colored agar containing different concentrations of antibiotics are overlaid by soft agar allowing bacterial motility.

Bacteria are inoculated at the end zones of the dish and initially grow in the absence of antibiotic. But eventually these bacterial Edens run out of nutrients, and to continue growing the bacteria must leave the garden for the cruel world outside. They only have one direction to go, into the nasty antibiotic. Eventually, a handful of bacteria manage it. Their progeny quickly fill the low-concentration region, then the next-lowest and so on:

It’s a living Muller plot! Muller plots are used to visualize evolutionary dynamics:

Figure 2c from Herron and Doebeli 2013. Muller plot showing E. coli evolution over 1200 generations, including all of the mutations. Hey, I’m cited in the Wikipedia page on Muller plots! REL 606 is the starting strain, three and four-letter codes, with the numbers identifying the amino acid position at which the mutation occurs. Mutations with two gene names (e.g. mokB/trg) indicate intergenic mutations, and delta with a number indicates a deletion and its length.

This is some of the coolest research I’ve seen lately, at least in a visual sense, and it does tell us something about how evolution plays out in spatially structured landscapes. So what is Dr. Hunter’s problem? I’ll try to summarize his argument briefly; bear in mind that the ellipses in some cases indicate skipping over large sections of text:

The experiment did not demonstrate evolution, it falsified evolution…bacteria adaptation research, over several decades now, has clearly shown non-evolutionary change…

…the Harvard experiment demonstrated, again, very rapid adaptation. In just ten days the bacteria adapted to high doses of lethal antibiotic…

The ability of organisms to adapt rapidly falls under the category of epigenetics, a term that encompasses a range of sophisticated mechanisms which promote adaptation which is sensitive to the environment. Given our knowledge of bacterial epigenetics, and how fast the bacteria responded in the Harvard experiment, it certainly is reasonable to think that epigenetics, of some sort, may have been at work.

Taken as a whole, these statements suggest that Dr. Hunter has not actually read the Baym et al. paper, has not read most of the literature on experimental microbial evolution, and lacks a basic understanding of the mechanisms of evolution. If he had read (well, read and understood) the paper, he would know that the researchers showed that the researchers identified the specific mutations responsible for the observed adaptations:

For instance, bacterial adaptation has often been found to be rapid, and sensitive to the environmental challenge.

Well, that much is true. But then his argument goes right off the rails:

The ability of organisms to adapt rapidly falls under the category of epigenetics, a term that encompasses a range of sophisticated mechanisms which promote adaptation which is sensitive to the environment. Given our knowledge of bacterial epigenetics, and how fast the bacteria responded in the Harvard experiment, it certainly is reasonable to think that epigenetics, of some sort, may have been at work.

It really isn’t. The whole reason the term epigenetics exists is to distinguish mechanisms like DNA methylation and histone modification from changes to the DNA sequence of the genome. And we know that the antibiotic resistance that arose in this experiment is due to changes in the DNA sequences of the bacteria. We know this because Baym et al. sequenced the bacterial genomes and identified the exact causative mutations.

The funny thing is that Dr. Hunter seems to know this:

Another problem, one that Michael Behe points out, is that it appears that most of the mutations that occurred in the experiment served to shutdown genes.

Okay, you can’t have it both ways. The changes were either due to changes in DNA sequences (mutations) or to epigenetics. Those are mutually exclusive categories. Epigenetic changes are by definition not mutations. In claiming that the antibiotic resistance is due to epigenetics and, at the same time, due to loss of function mutations, Dr. Hunter is not only ignoring the evidence that the changes are genetic, he’s contradicting himself.

But he’s not done with his fundamental misunderstandings of his claimed area of expertise:

In other words, the mutations broke things, they did not build things. This is another way to see that this does not fit the evolutionary model. It’s devolution, not evolution.

As Dr. Novella points out, devolution isn’t a thing. Yes, evolution sometimes proceeds by selection or drift on loss of function mutations. It’s still evolution. Evolution (in this case) by natural selection.The whole idea of ‘devolution’ is based on progressivist misconceptions of what evolution is.

…it is not Behe here who is making the mistake, it is Novella. He says “Evolution is simply heritable change…” But this is an equivocation.

On the one hand, evolutionists want to say that shutting down or slowing a gene is “evolution,” but on the other hand, they say that a fish turning into a giraffe is “evolution.”

Unfortunately evolutionists routinely make this equivocation. This is because they don’t think of it as an equivocation. In their adherence and promotion of the theory, the distinction is lost on them.

We don’t think of it as an equivocation because it’s not. Heritable change is exactly what evolution is, and it explains both the loss or reduction of gene functions by selection and the descent of giraffes from fish ancestors. The ‘distinction’ Dr. Hunter is looking for is that one of those processes is evolution over a period of days, and the other is evolution over hundreds of millions of years.

I wonder if Dr. Hunter realizes that, in his defense of Dr. Behe, he is contradicting Dr. Behe’s own views. In contrast to Dr. Hunters claim that microbial evolution experiments falsify evolution, Dr. Behe calls the Long-Term Evolution Experiment

…the best, most detailed source of information on evolutionary processes available anywhere, dwarfing rival lab projects and swamping field studies. That’s an achievement well worth celebrating.

He has also said (in The Edge of Evolution) that

…there’s also great evidence that random mutation paired with natural selection can modify life in important ways

and that

…wherever there is variation, selection, and inheritance, then there absolutely must be evolution.

Dr. Hunter doesn’t understand the basic mechanisms of evolution. He doesn’t understand what epigenetics is, and he thinks loss of function mutations are an example of epigenetic change. He thinks adaptation is not an example of evolution. He thinks that microbial experiments, in which mutations can be directly observed to increase due to selection, disprove evolution. All this in spite of his claimed expertise “specifically in evolution.” Michael Behe, from the evidence of his own words, agrees with none of these things. I look forward to seeing him set his Discovery Institute colleague straight.